M Bernt

Document meaning of `Use POSIX standard` in upload options.

1

**Describe the bug** This is very technical and should be explained to end users. See 3.206 in https://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap03.html For fact I always assumed that this just converts `\r\n` to `\n`,...

History deletion wording inconsistency

6

**Describe the bug** The history menu entry _Delete this history_ has a tooltip _Permanently delete this history_ - _Permanently_ should be removed from the tooltip (because permanence is only optional)...

length parameters should not be optional - add test for dada2 using no value for the length parameter

add old datamash

1

Trying to get rid of conda envs. Need a container for an old version of: https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash

Allow modes `z` and `Z` for docker volumes

4

Fixes https://github.com/galaxyproject/galaxy/issues/18989 ## How to test the changes? (Select all options that apply) - [x] I've included appropriate [automated tests](https://docs.galaxyproject.org/en/latest/dev/writing_tests.html). - [ ] This is a refactoring of components with...

- `data_ref` needs to be specified in the XML - `data_ref` needs to refer to an existing parameter Fixes https://github.com/galaxyproject/galaxy/issues/18359 (i.e. the misleading error message, since now the `KeyError` caused...

TS Error when creating new repo

1

**Describe the bug** The following error suggests a problem with a data table .. but the tool has none: ``` HTTP status code: 500: {"err_msg": "Metadata may have been defined...

This will allow to overwrite `real_system_username` per destination. There are two places in the code left where still the global config is used: - https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/imp_exp/__init__.py - https://github.com/galaxyproject/galaxy/blob/9e01e37bc19abe0fc6ec91497bb5e7c6a9c83daa/lib/galaxy/tools/actions/upload_common.py For my use...

[24.1] Remove defaults channel for conda usage

11

To get rid of the potential problem with the default channel in planemo usage and up-to-date installations I would suggest a backport. Instead of 24.1 we could also got further...

msnbase needs fortran requirement

1

Seems that we need a fortran requirement for msnbase ... or is it something different like gcc? ``` library(MSnbase) Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’...